Table 2.
dn/ds Ratio at the Per Codon Level for Tat Exon 1 Sequences
| SAR | ||||||
|---|---|---|---|---|---|---|
| Amino acid position | Syn | Nonsyn | dn/ds ratio | Evolutionary selection | Amino acid | selection |
| D5 | 0.13 | 0.05 | 0.38 | Purifying | — | |
| N12 | 0.29 | 0.21 | 0.72 | Purifying | — | |
| A21 | 0.03 | 0.13 | 4.33 | Positive | — | |
| N23 | 0.08 | 0.19 | 2.38 | Positive | — | |
| N24 | 0.28 | 0.33 | 1.18 | Positive | — | |
| Y26 | 0.17 | 0.49 | 2.88 | Positive | — | |
| K29 | 0.06 | 0.6 | 10.00 | Positive | H | Negative |
| C30 | 0.31 | 0.03 | 0.10 | Purifying | — | |
| S31 | 0.05 | 0.21 | 4.20 | Positive | S | Positive |
| Y32 | 0.23 | 0.03 | 0.13 | Purifying | ||
| L35 | 0.06 | 0.24 | 4.00 | Positive | L | Positive |
| V36 | 0.04 | 0.29 | 7.25 | Positive | — | |
| Q39 | 0.07 | 0.21 | 3.00 | Positive | Q | Positive |
| K40 | 0.15 | 0.55 | 3.67 | Positive | — | |
| G44 | 0.19 | 0.03 | 0.16 | Purifying | — | |
| Q54 | 0.04 | 0.12 | 3.00 | Positive | — | |
| R56 | 0.05 | 0.03 | 0.60 | Purifying | — | |
| T57 | 0.05 | 0.52 | 10.40 | Positive | S | a |
| Q60 | 0.47 | 0.61 | 1.30 | Positive | P | Negative |
| S61 | 0.1 | 0.25 | 2.50 | Positive | — | |
| S62 | 0.03 | 0.05 | 1.67 | Positive | — | |
| E63 | 0.13 | 0.17 | 1.31 | Positive | E | Positive |
| D64 | 0.15 | 0.32 | 2.13 | Positive | — | |
| I68 | 0 | 0.72 | — | L | a | |
The dn/ds ratio at each codon was evaluated using the SNAP version 2.1.1 (Synonymous Nonsynonymous Analysis Program) tool available at HIV-LANL. The selection pressure deduced by the dn/ds ratio was compared with the selection that was suggestive from the VESPA of the changing profile of the SAR at specific locations.
a
T57 and I68 are seen only in the case of one subject each, that is, 2067-M0 and 2081-M0, respectively.
SAR, signature amino acid residue; VESPA, Viral Epidemiological Signature Pattern Analysis.